Fusion Balls are without a doubt the most devasting weapon per shot available for use on X-COM craft. They have the greatest range of any X-COM craft weapon, standing at 65 km. They also have the highest firepower - damage per unit of time - of any craft weapon in the game, including alien weapons. Until they run out of ammunition, that is.

However, the drawbacks associated with Fusion Balls in general outweigh the advantages. There is only enough room on each hardpoint to load two fusion balls into each launcher, for a total of four shots. Against most UFOs, this is more than adequate; but against alien Battleships , a lone craft or even a pair of craft will likely run out of ammunition before bringing it down.
The FBL also requires ammo to be manufactured for it, at a HIGH cost of hours (21000 dollars worth of labour) , cash (28000) and Elerium (4 elerium... market price 20000 but worth much more than that). EACH.
The FBL does 230 maximum damage vs the Plasma Beam's 140, but has a minimum reload time of 16gs/24gs/32gs, vs PB 12gs.
The FBL has 2 shots, the PB has 99.
Fortunately, the FBL has 100% accuracy, compared to PB with 50%.

Although it has the greatest range of all X-COM craft weapons, it is only equal to the range of the craft weapon on an alien Battleship. However, the Plasma Beam and Avalanche outrange all other UFOs except Battleships. This makes the FBL's range advantage over the Plasma Beam and Avalanche largely redundant, though it does reduce the amount of time spent being fired upon without being able to fire back.

Despite these disadvantages, however, Fusion Balls are the safest way to intercept Battleships using Interceptors. You'll still probably lose some of the Interceptors, along with their valuable armament, so this is really reserved for the last resort.